Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012264.1 Corchorus olitorius cultivar O-4 contig12297, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 40935
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1290 original size:29 final size:29
Alignment explanation
Indices: 1248--1306 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1238 AACAAATTTT
1248 ATTCGTGAGACAATCAAGATTATCCTTGG
1 ATTCGTGAGACAATCAAGATTATCCTTGG
1277 ATTCGTGAGACAATCAAGATTATCCTTGG
1 ATTCGTGAGACAATCAAGATTATCCTTGG
1306 A
1 A
1307 CTAATGCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (29 bp):
ATTCGTGAGACAATCAAGATTATCCTTGG
Found at i:3361 original size:13 final size:13
Alignment explanation
Indices: 3343--3367 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3333 TTGCTACATT
3343 AAAAAAAAGGAAA
1 AAAAAAAAGGAAA
3356 AAAAAAAAGGAA
1 AAAAAAAAGGAA
3368 GTTAATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGGAAA
Found at i:4311 original size:2 final size:2
Alignment explanation
Indices: 4304--4332 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4294 ATAACTTTAA
4304 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4333 ATACTAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6491 original size:6 final size:6
Alignment explanation
Indices: 6480--6505 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6470 AATATATAAG
6480 AAAACA AAAACA AAAACA AAAACA AA
1 AAAACA AAAACA AAAACA AAAACA AA
6506 TTTGAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACA
Found at i:11288 original size:332 final size:331
Alignment explanation
Indices: 10295--11473 Score: 1388
Period size: 331 Copynumber: 3.5 Consensus size: 331
10285 TCCTTTGTTA
* * * * *
10295 CAAAAAACTGTGATGGTTAATACACGATTTCGGTTAAAATTTTGCAAAAATTTATCCGAAAGAAT
1 CAAAAATC-GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-AAT
* * * *
10360 TT-TCCT-AATTTTTTTGCCATGATACTCATGAAAAATATATAATTAAACGCCAAAAAGATTGAA
64 TTCTCCTCAA-TTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAA
* * *
10423 AGGCTTT-TCACGTTTCTAATATCGGTTTTCTTAATTTTTCCGAATTAATTTCTAATTAAATCGA
128 AGGCTTTCTCACGCTTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCGA
* *
10487 AACATGATTCAGATGCTCGTAAAAACAAATTCTTAAATTCAATGTGGTTGAGATTTGGTTAGATG
193 AACATGATTCAGATGCTCGTAAAAACAAA-TCTTAAATCCAATGTGGCTGAGATTTGGTTAGATG
* * * * *
10552 GATATAGATATTTCAATGAGACTTAGCGCCAAAAATCATGCAAAATAGAGTCGGGA-CCCCGAAT
257 AATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAG-CTGGAGCCCAGAA-
10616 CGCATTTTTAGT
320 CGCATTTTTAGT
* *
10628 CAAAACT-GTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCTAAAAA-TGACAC-AAAACAT
1 CAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGC-AAAAATTGACCCGAAAA-AT
** * * *
10690 TTCTCCTCAATTTCCGGCCACCATATTCATAAAAAATATA-AA-TCAACGCCAAAAA-ATTGAAG
64 TTCTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAA
** * * *
10752 GGC-TTCTCATACTTCTAATATTGTTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATC
129 GGCTTTCTCACGCTTCTAATATCG---TTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATC
** * * *
10816 GAAACCGGATTGAGATGCTCGTAAAAA-AAATCCTTAAATCTAATGTGGCTGAGATTTCGTTAGA
191 GAAACATGATTCAGATGCTCGTAAAAACAAAT-CTTAAATCCAATGTGGCTGAGATTTGGTTAGA
* * * *
10880 TAAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG-TCGGGGCCACAG
255 TGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCT-GGAGCC-CAG
10944 AACGCATTTTTAG-
318 AACGCATTTTTAGT
* *
10957 CGAAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGAAT
1 C-AAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAA-AAT
* * * *
11022 TT-TCCTCAATTTTTGGCCACGATACTCATAAAAAATTTATTATTCAACACCAAAAGGATTGAAA
64 TTCTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAA
* * * * * * * *
11086 GGCTAT-TCACGCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTCCTAATTGAACCAAA
129 GGCTTTCTCACGCTTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCGAA
* * *
11150 ACATGATTCATATGCTCGTAAAAACAAATCATTAAATCCAATGTGGGTAAGATTTGGTTAGATGA
194 ACATGATTCAGATGCTCGTAAAAACAAATC-TTAAATCCAATGTGGCTGAGATTTGGTTAGATGA
11215 ATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCTGGAGCTCCAGAACG
258 ATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCTGGAGC-CCAGAACG
*
11280 CGTTTTTAGT
322 CATTTTTAGT
** * * *
11290 CAAAAGCCGTGATGG-TAGTGCACGATTTCAGCTAAAATTTTGCAAAAATTGACCCGAGAAATTT
1 CAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTT
* * * * *
11354 CTCCTCAATTTTGGGCCAC-ACTACTAATAAGAAATATATAACTCAACGCCAAAAAGACTG-AAG
66 CTCCTCAATTTTTGGCCACGA-TACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAG
* *
11417 GGTTTCTCACGACGCTTCTAATATCGTTTTTCCTACATTTTCCCGAATTAATTTCTA
130 GCTTTCT--C-ACGCTTCTAATATCGTTTTTCCTA-ATTTTTCCGAATTAATTTCTA
11474 GTTGAAAAAT
Statistics
Matches: 713, Mismatches: 100, Indels: 64
0.81 0.11 0.07
Matches are distributed among these distances:
327 2 0.00
328 22 0.03
329 17 0.02
330 121 0.17
331 342 0.48
332 125 0.18
333 21 0.03
334 45 0.06
335 18 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (331 bp):
CAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAATTT
CTCCTCAATTTTTGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGG
CTTTCTCACGCTTCTAATATCGTTTTTCCTAATTTTTCCGAATTAATTTCTAATTAAATCGAAAC
ATGATTCAGATGCTCGTAAAAACAAATCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATA
TAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACAGAGCTGGAGCCCAGAACGCATT
TTTAGT
Found at i:11700 original size:96 final size:97
Alignment explanation
Indices: 11521--11703 Score: 296
Period size: 98 Copynumber: 1.9 Consensus size: 97
11511 AAATATATTT
* * * *
11521 GAAAAAAAGTACACAAAATTATATTTTAATAATGGCATAGTTAAAATATGTTTTAATAATGATAA
1 GAAAAAAAATACACAAAATTATATTTTAATAATGACATAATTAAAATA-GTTTTAATAATGACAA
11586 TTTAAAAATATATTTGAAAAAATAGTAAAATCG
65 TTTAAAAATATATTTGAAAAAATAGTAAAATCG
*
11619 GAAAAAAAATACATAAAATTATATTTTAATAATGACATAATTAAAATA-TTTTAATAATGACAAT
1 GAAAAAAAATACACAAAATTATATTTTAATAATGACATAATTAAAATAGTTTTAATAATGACAAT
*
11683 TTAGAAATATATTTGAAAAAA
66 TTAAAAATATATTTGAAAAAA
11704 GGGGTATAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
96 35 0.44
98 44 0.56
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.34
Consensus pattern (97 bp):
GAAAAAAAATACACAAAATTATATTTTAATAATGACATAATTAAAATAGTTTTAATAATGACAAT
TTAAAAATATATTTGAAAAAATAGTAAAATCG
Found at i:11994 original size:21 final size:22
Alignment explanation
Indices: 11835--12037 Score: 94
Period size: 22 Copynumber: 9.2 Consensus size: 22
11825 GATAACCACC
*
11835 AAATTTTGATAA-CTACACTATG
1 AAATTTTGATAACCT-CCCTATG
* *
11857 AAATTTTGATGA-TTACCCTATG
1 AAATTTTGATAACCT-CCCTATG
* * * * *
11879 AAACTGTGATAAACTCCCAAGG
1 AAATTTTGATAACCTCCCTATG
** ** *
11901 AAATACTGATAACCTAACTATA
1 AAATTTTGATAACCTCCCTATG
* * **
11923 AAATTTTAATAAACTTTTCTATG
1 AAATTTTGAT-AACCTCCCTATG
*
11946 AAATTTTGATAACCTCTCTATG
1 AAATTTTGATAACCTCCCTATG
*
11968 AAATTTT-ATTAATCTCCCTAT-
1 AAATTTTGA-TAACCTCCCTATG
**
11989 AAATTTTTGAT-ACCAT-AATATG
1 AAA-TTTTGATAACC-TCCCTATG
* * *
12011 AAATTTCGATAATCTCTCTATG
1 AAATTTTGATAACCTCCCTATG
12033 AAATT
1 AAATT
12038 ATATATCATT
Statistics
Matches: 135, Mismatches: 37, Indels: 18
0.71 0.19 0.09
Matches are distributed among these distances:
21 16 0.12
22 100 0.74
23 19 0.14
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATG
Found at i:13000 original size:2 final size:2
Alignment explanation
Indices: 12993--13045 Score: 53
Period size: 2 Copynumber: 29.0 Consensus size: 2
12983 TTCGTACTTG
* *
12993 TA TA TA TA T- TA TA GA TA TA GA TA TA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13032 -A TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA
13046 CACACACAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
1 5 0.12
2 37 0.88
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:13027 original size:5 final size:5
Alignment explanation
Indices: 12996--13045 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
12986 GTACTTGTAT
*
12996 ATATA TTATA GATATA GATAT- ATATA ATATA ATATA ATATA ATAT- ATATA
1 ATATA ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA
13046 CACACACAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
4 8 0.20
5 23 0.57
6 9 0.22
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:13328 original size:60 final size:59
Alignment explanation
Indices: 13251--13417 Score: 203
Period size: 60 Copynumber: 2.8 Consensus size: 59
13241 GACTAATTGC
* * ** *
13251 TCAAATTAAGGTCCTAACGTTTGTC-AAAATGTTCAAATAAGGGTTTGATCTTTTAATTTGG
1 TCAAA-TAAGGT-CTAACG-TTATCGAAAATGCTCAAATAAGGGCCTGATATTTTAATTTGG
13312 -CTAAATAAAGGTCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATATTTTAATTTGG
1 TC-AAAT-AAGGTCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATATTTTAATTTGG
* *
13372 TCAAATAAGGATCTAACATTATCGAAAATGCTCAAATAAGGACCTG
1 TCAAATAAGG-TCTAACGTTATCGAAAATGCTCAAATAAGGGCCTG
13418 GCGTCGAAAA
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
59 8 0.09
60 77 0.82
61 9 0.10
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (59 bp):
TCAAATAAGGTCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATATTTTAATTTGG
Found at i:13410 original size:31 final size:31
Alignment explanation
Indices: 13314--13413 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
13304 TAATTTGGCT
*
13314 AAATAAAGG-TCTAACGTTATCGAAAATGCTC
1 AAAT-AAGGATCTAACATTATCGAAAATGCTC
** * * * ** *
13345 AAATAAGGGCCTGATATT-T-TAATTTGGTC
1 AAATAAGGATCTAACATTATCGAAAATGCTC
13374 AAATAAGGATCTAACATTATCGAAAATGCTC
1 AAATAAGGATCTAACATTATCGAAAATGCTC
13405 AAATAAGGA
1 AAATAAGGA
13414 CCTGGCGTCG
Statistics
Matches: 50, Mismatches: 16, Indels: 6
0.69 0.22 0.08
Matches are distributed among these distances:
29 20 0.40
30 6 0.12
31 24 0.48
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (31 bp):
AAATAAGGATCTAACATTATCGAAAATGCTC
Found at i:13555 original size:60 final size:60
Alignment explanation
Indices: 13460--13619 Score: 155
Period size: 60 Copynumber: 2.7 Consensus size: 60
13450 ACGTCAGGCT
* *
13460 CTTATTTGAGCATTTTCGATAACATTAGACTCTTATTTGGCCAAATTAAAAGATCAGAC-C
1 CTTATTTGAGCATTTTCGATAACATTAGACCCTTATTTGACCAAATTAAAAGAT-AGACTC
** * * * * * *
13520 CTTATTTGAGCATTTTTTAT-ACTGTTAGGCCCTTATTTGATCAGATTAAAAGATTGGCTC
1 CTTATTTGAGCATTTTCGATAAC-ATTAGACCCTTATTTGACCAAATTAAAAGATAGACTC
* * *
13580 CTTATTTGAACATTTT-GAAAAACATTAGGCCCTTATTTGA
1 CTTATTTGAGCATTTTCG-ATAACATTAGACCCTTATTTGA
13620 GAATTAGTTA
Statistics
Matches: 82, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
59 4 0.05
60 76 0.93
61 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (60 bp):
CTTATTTGAGCATTTTCGATAACATTAGACCCTTATTTGACCAAATTAAAAGATAGACTC
Found at i:13617 original size:31 final size:29
Alignment explanation
Indices: 13544--13619 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
13534 TTTTATACTG
* *
13544 TTAGGCCCTTATTTGATCAGATTAAAAGA
1 TTAGGCCCTTATTTGAACAGATTAAAACA
**
13573 TT-GGCTCCTTATTTGAACATTTTGAAAAACA
1 TTAGGC-CCTTATTTGAACAGATT--AAAACA
13604 TTAGGCCCTTATTTGA
1 TTAGGCCCTTATTTGA
13620 GAATTAGTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.08
29 16 0.41
31 17 0.44
32 3 0.08
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (29 bp):
TTAGGCCCTTATTTGAACAGATTAAAACA
Found at i:14678 original size:107 final size:109
Alignment explanation
Indices: 14546--14762 Score: 348
Period size: 107 Copynumber: 2.0 Consensus size: 109
14536 GTACAAGTTG
* * * * *
14546 ATCGGCTCACGCTGGCGCGTTGAGCATTCTTGATTTGTGGCTAGCAAATTATTTTAGTTTTAGAG
1 ATCGGCTCACGCTGGCGCGTCGAGCATTCTTAATATGTGGCTAGCAAATCATTTTAGTTATAGAG
*
14611 -TTTTTTTT-TCTCGGTTCTTATCATATATGTGAGTAGGTGGTT
66 TTTTTTTTTCTCTCGATTCTTATCATATATGTGAGTAGGTGGTT
**
14653 ATCGGCTTGCGCTGGCGCGTCGAGCATTCTTAATATGTGGCTAGCAAATCATTTTAGTTATAGAG
1 ATCGGCTCACGCTGGCGCGTCGAGCATTCTTAATATGTGGCTAGCAAATCATTTTAGTTATAGAG
14718 TTTTTTTTTCTCTCGATTCTTATCATATATGTGAGTAGGTGGTT
66 TTTTTTTTTCTCTCGATTCTTATCATATATGTGAGTAGGTGGTT
14762 A
1 A
14763 ACAAATTTGA
Statistics
Matches: 100, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
107 58 0.58
108 8 0.08
109 34 0.34
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (109 bp):
ATCGGCTCACGCTGGCGCGTCGAGCATTCTTAATATGTGGCTAGCAAATCATTTTAGTTATAGAG
TTTTTTTTTCTCTCGATTCTTATCATATATGTGAGTAGGTGGTT
Found at i:15572 original size:2 final size:2
Alignment explanation
Indices: 15565--15609 Score: 74
Period size: 2 Copynumber: 22.5 Consensus size: 2
15555 TAATATTTAG
15565 TA TA TA TA TA TA TA TA TA T- TA GTA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
15607 TA T
1 TA T
15610 TAGTAGACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.02
2 38 0.93
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15587 original size:22 final size:22
Alignment explanation
Indices: 15557--15605 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
15547 CTTTCAAATA
15557 ATAT-TTAGTATATATATATAT
1 ATATATTAGTATATATATATAT
15578 ATATATTAGTATATATATATAT
1 ATATATTAGTATATATATATAT
15600 ATATAT
1 ATATAT
15606 ATATTAGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
ATATATTAGTATATATATATAT
Found at i:16472 original size:18 final size:18
Alignment explanation
Indices: 16423--16460 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16413 GGGGGAGGAG
16423 GAGGATTTCGTTTTGGTT
1 GAGGATTTCGTTTTGGTT
16441 GAGGATTTCGTTTTGGTT
1 GAGGATTTCGTTTTGGTT
16459 GA
1 GA
16461 TTTCTTCGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.05, G:0.34, T:0.47
Consensus pattern (18 bp):
GAGGATTTCGTTTTGGTT
Found at i:16535 original size:16 final size:18
Alignment explanation
Indices: 16516--16554 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
16506 GTTTTTTTTT
16516 AGTTTG-TTTTT-GAGTC
1 AGTTTGTTTTTTCGAGTC
*
16532 AGTTCGTTTTTTCGAGTC
1 AGTTTGTTTTTTCGAGTC
16550 AGTTT
1 AGTTT
16555 CGAGTCTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.13, C:0.10, G:0.23, T:0.54
Consensus pattern (18 bp):
AGTTTGTTTTTTCGAGTC
Found at i:17474 original size:11 final size:11
Alignment explanation
Indices: 17460--17497 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
17450 ATTCATAACA
17460 AATTTATAATT
1 AATTTATAATT
17471 AATTTATAATT
1 AATTTATAATT
17482 -ATTTGATAATT
1 AATTT-ATAATT
*
17493 TATTT
1 AATTT
17498 TATATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:18979 original size:26 final size:26
Alignment explanation
Indices: 18949--19000 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
18939 TATATGGTGA
18949 GGCCATATAAATGAGTATATATATAT
1 GGCCATATAAATGAGTATATATATAT
*
18975 GGCCATATAAATGAGTATATGTATAT
1 GGCCATATAAATGAGTATATATATAT
19001 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (26 bp):
GGCCATATAAATGAGTATATATATAT
Found at i:19434 original size:42 final size:43
Alignment explanation
Indices: 19382--19475 Score: 147
Period size: 45 Copynumber: 2.2 Consensus size: 43
19372 AGTGCATTAT
*
19382 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
19423 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
19468 CTAATATT
1 CTAATATT
19476 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
41 4 0.08
42 6 0.12
45 38 0.79
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:22253 original size:13 final size:13
Alignment explanation
Indices: 22235--22259 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22225 CAATTCCTTG
22235 TTAATTTTTTATT
1 TTAATTTTTTATT
22248 TTAATTTTTTAT
1 TTAATTTTTTAT
22260 AGGCCGCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTAATTTTTTATT
Found at i:28658 original size:21 final size:20
Alignment explanation
Indices: 28619--28663 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28609 AAATAACAAT
* *
28619 TAAAAACAAAGCAATTAAAC
1 TAAAAACAAAGAAAGTAAAC
*
28639 TAAAAACAAAGTAAAGTAAAT
1 TAAAAACAAAG-AAAGTAAAC
28660 TAAA
1 TAAA
28664 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.07, T:0.18
Consensus pattern (20 bp):
TAAAAACAAAGAAAGTAAAC
Found at i:33423 original size:39 final size:39
Alignment explanation
Indices: 33369--33445 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
33359 CACGAGCCAC
*
33369 CAAAACAGTCCAGCTCAAGAGAAGCAAAAGCAAACAGAG
1 CAAAACAGTCCAGCTCAAGAGAAACAAAAGCAAACAGAG
*
33408 CAAAACTGTCCAGCTCAAGAGAAACAAAAGCAAACAGA
1 CAAAACAGTCCAGCTCAAGAGAAACAAAAGCAAACAGA
33446 AGGAGGACAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.52, C:0.23, G:0.18, T:0.06
Consensus pattern (39 bp):
CAAAACAGTCCAGCTCAAGAGAAACAAAAGCAAACAGAG
Done.